BBDuk error: with these 4 lines....

Question

[blackadder]

Hello there,

I am trying to trim some samples with BBDuk and I am getting this error:

Error in /home/projects/Raw_data/sample1_L001_R2_001.fastq.gz , line 120314999, with these 4 lines: + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFTTACTGAGCAAATAAATAGACTCTATATTGTCTCCG ATGGCATAAAAATGTGTTTGTGGAAAAGCAATCCTTAAATTGAGAAAACGTTTTATATTAGGGCCAATGATAGGATAAGCAAGTAATACATCTGTAGCA + FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFTTACTGAGCAAATAAATAGACTCTATATTGTCTCCG ATGGCATAAAAATGTGTTTGTGGAAAAGCAATCCTTAAATTGAGAAAACGTTTTATATTAGGGCCAATGATAGGATAAGCAAGTAATACATCTGTAGCA

 at stream.FASTQ.quadToRead_slow(FASTQ.java:708)
 at stream.FASTQ.toReadList(FASTQ.java:659)
  at stream.FastqReadInputStream.fillBuffer(FastqReadInputStream.java:107)
  at stream.FastqReadInputStream.nextList(FastqReadInputStream.java:93)
   at stream.ConcurrentGenericReadInputStream$ReadThread.readLists(ConcurrentGenericReadInputStream.java:681)
   at stream.ConcurrentGenericReadInputStream$ReadThread.run(ConcurrentGenericReadInputStream.java:657)

Processing time: 1085.136 seconds.

Input: 60146000 reads 9082046000 bases. QTrimmed: 15227591 reads (25.32%) 749311115 bases (8.25%) KTrimmed: 162532 reads (0.27%) 5528191 bases (0.06%) Trimmed by overlap: 138767 reads (0.23%) 1264556 bases (0.01%) Total Removed: 2944724 reads (4.90%) 756103862 bases (8.33%) Result: 57201276 reads (95.10%) 8325942138 bases (91.67%)

Time: 1085.209 seconds. Reads Processed: 60146k 55.42k reads/sec Bases Processed: 9082m 8.37m bases/sec Exception in thread "main" java.lang.RuntimeException: jgi.BBDuk terminated in an error state; the output may be corrupt. at jgi.BBDuk.process(BBDuk.java:1101) at jgi.BBDuk.main(BBDuk.java:81)

I looked online for people with similar problems but I couldnt find anything.

This is the BBDuk flags im using:

qin="auto", k="19", ref="adapters", mink="11", qtrim="r", trimq="20", minlength="50", ziplevel="6", overwrite="t", statscolumns="5", ktrim="r

Thanking you in advance!

Answer 1

[Pierre Lindenbaum]

looks like your fastq file is corrupted. Those 4 lines don't look like a fastq record:

+ FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFTTACTGAGCAAATAAATAGACTCTATATTGTCTCCG ATGGCATAAAAATGTGTTTGTGGAAAAGCAATCCTTAAATTGAGAAAACGTTTTATATTAGGGCCAATGATAGGATAAGCAAGTAATACATCTGTAGCA
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFTTACTGAGCAAATAAATAGACTCTATATTGTCTCCG ATGGCATAAAAATGTGTTTGTGGAAAAGCAATCCTTAAATTGAGAAAACGTTTTATATTAGGGCCAATGATAGGATAAGCAAGTAATACATCTGTAGCA

it looks like a mix of SEQ and QUAL, the first line should start with '@', etc...

count the number of lines in the fastq,

look at the lines in the region of line 120314999 in /home/projects/Raw_data/sample1_L001_R2_001.fastq.gz

[Meisam]

Up this answer. Just wanted to add reminder that it is good habit to do quality check before and after any analysis step, simply using FASTQC it can pick up corrupt files.

[blackadder]

Thank you for the response!